BIO - CH 18 Regulation of Gene Expression

What has natural selection favored?

bacteria that produce only the products needed by that cell

How can a cell regulate the production of enzymes?

by feedback inhibition or by gene regulation

How is gene expression controlled in bacteria?

by the operon model

In bacteria, how can clusters of functionally related genes be under coordinated control?

by a single on-off switch

What is an operator?

the segment of DNA that is a regulatory switch that is usually positioned within the promoter

What is an operon?

an operon is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control

How can an operon be switched off?

by a protein repressor

What does a protein repressor do?

the repressor prevents gene transcription by binding to the operator and blocking RNA polymerase

What is a repressor a product of?

a separate regulatory gene

Depending on the presence of other molecules, what can a repressor be?

active or inactive

What is a corepressor?

a molecule that cooperates with a repressor protein to switch an operon off

Information about the trp operon

- by default the trp operon is on and the genes for tryptophan synthesis is transcribed
- when tryptophan is present, it binds to the trp respressor protein which turns the operon off
- the repressor is active only in the presensce of its corepressor tryptophan; thus the trp operon is turned off (repressed) if tryptophan level are high

A repressible operon is one that what?

one that is usually on; binding of a repressor to the operator shuts off transcription

What is the trp operon?

it is a repressible operon

An inducible operon is one that what?

is usually off; a molecule called an inducer inactivates the repressor and turns on transcription

What is an inducer?

a molecule that inactivates the repressor

When do inducible enzymes usually function?

in catabolic pathways; their synthesis is induced by a chemical signal

When do repressible enzymes usually function?

in anabolic pathways' their synthesis is repressed by high levels on the end product

What does regulation of the trp and lac operons involve?

negative control of genes because operons are switched off by the active form of the repressor

What is catabolite activator protein (CAP)?

- an operon that is subject to positive control through a stimulatory protein
- its an activator of protein

When glucose (the preferred food source of E. coli) is scarce, what happens to CAP?

CAP is activated by binding with cyclic AMP (cAMP) which accumulated when glucose is scarce & the activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription

What is chromatin modification?

DNA unpacking involving histone acetylation and DNA demethylation

What happens to genes with highly packed heterochromatin?

they are usually not expressed

What do chemical modifications to histones and DNA of chromatins influence?

they influence both chromatin structure and gene expression

What is differential gene expression?

the expression of different genes by cells with the same genome

What can abnormalities in gene expression lead to?

diseases including cancer

What is histone acetylation?

when acetyl groups are attached to positively charged lysines in histone tails

What does histone acetylation do?

it loosens chromatin structure, thereby promoting the initiation of transcription

What addition can condense chromatin?

the addition of methyl groups (methylation)

What addition can loosen chromatin?

the addition of phosphate groups (phosphorylation)

When does acetylation happen in the cell cycle?

in S phase, prophase: condensed chromosomes, first phase of mitosis

What does the histone code hypothesis propose?

that "specific combination of modifications, as well as the order in which they occur," help determine chromatin configuration and influence transcription

What happens in DNA methylation?

the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in many species

What can DNA methylation cause?

long-term inactivation of genes in cellular differentiation

What does methylation regulate in genomic imprinting?

methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development

In genomic imprinting or other epigenetic states, where is methylation?

at regions of potential methylation called CpG islands

What is epigenetic inheritance?

the inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence

How does chromatin-modifying enzymes provide initial control of gene expression?

by making a region of DNA either more or less able to bind the transcription machinery

What happens to the DNA is there is a row methylated CpG sites?

the DNA is inaccessible to binding proteins

What are control elements?

they are segments of noncoding DNA that serve as binding sites for transcription factors that help regulate transcription

Control elements and the transcription factors they bind to are critical to what?

the precise regulation of gene expression in different cell types

What needs to happen to initiate transcription?

eukaryotic RNA polymerase requires the assistance of proteins called transcription factors

What are essential for the transcription of all protein-coding genes?

general transcription factors

In eukaryotes, what do high levels of transcription depend on?

control elements interacting with specific transcription factor

Where proximal control elements located?

close to the promoter

What are enhancers?

distal control elements that may be far away from a gene or even located in an intron

What is an activator?

a protein that binds to an enhancer and stimulates transcription of a gene

What are the two domains of activators?

one that binds to DNA and a second that activates transcription

What do bound activators facilitate a sequence of?

protein-protein interactions that result in transcription of a given gene

When some transcription factors function as repressors, what do they inhibit?

the expression of a particular gene by a variety of methods

How to some activators and repressors act indirectly?

by influencing chromatin structure to promote or silence transcription

What can a particular combination of control elements activate?

transcription only when the appropriate activator proteins are present

Unlike the genes of a prokaryotic operon, each of the co-expressed eukaryotic genes have what?

a promoter and control elements

Where do loops of chromatin extend?

from individual chromosomes into specific sites in the nucleus

When loops from different chromosomes congregate at particular sites, what are they rich of?

they are rich in transcription factors and RNA polymerases which are ares that may be specialized for a common function

Does transcription alone account for genes expression?

no

What can operate at various stages after transcription?

regulatory mechanisms

What happens in alternative RNA splicing?

different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns

What is a key to determining protein synthesis?

the life span of mRNA molecules in the cytoplasm

Is eukaryotic or prokaryotic mRNA more long lived?

eukaryotic

Where do nucleotide sequences that influence the lifespan of mRNA in eukaryotes reside in?

the untranslated region (UTR) at the 3' end of the molecule

How can the initiation of translation of selected mRNAs be blocked?

by regulatory proteins that bind to sequences or structures of the mRNA

When translation initiation factors are simultaneously activated in an egg following fertilization, what is this an example of?

this is an example of translation of all mRNAs in a cell being regulated simultaneously

What is subject to control after translation?

various types of protein processing, including cleavage and the addition of chemical groups

What are proteasomes?

they are giant protein complexes that bind protein molecules and degrade them

Where do noncoding RNAs regulate gene expression?

at two points: mRNA translation and chromatin configuration

What are microRNAs (mrRNAs)?

they are small single-stranded sncRNA molecules that can bind to mRNA that can degrade mRNA or block its translation

What is RNA interference (RNAi)?

the phenomenon of inhibition of gene expression by RNA molecules

What is RNA interference (RNAi) caused by?

small interfering RNAs (siRNAs)

siRNAs and miRNAs are similar but form different what?

RNA precursors

In some yeasts, what role does siRNAs play?

they play a role in heterochromatin formation and can block large regions of the chromosome

What do sncRNAs called piwi-associated RNAs (piRNAs) do?

they induce heterochromatin, blocking the expression of "parasitic" DNA elements in the genome known as transposons

What can transposons act as?

transposable elements, moving blocks of DNA within and between chromosomes

What contains the most incRNAs?

sperm

What are cell types organized into?

tissues, organs, organ systems, and the whole organism

The transformation from zygote to adult results from what?

cell division, cell differentiation, and morphogenesis

What is cell differentiation?

the process by which cells become specialized in structure and function

The physical processes that give an organism its shape is called what?

morphogenesis

Differential gene expression results from what?

genes being regulated differently in each cell type

What does the egg's cytoplasm contain?

RNA, proteins, and other substances that are distributed unevenly in the unfertilized egg

What are cytoplasmic determinants?

maternal substances in the egg that influence early development - may also influence IncRNAs

What is fertilization?

the formation of a diploid zygote from a haploid egg and sperm

What happens when the sperm first touches the egg?

sperm penetrate the protective layer around the egg & receptors on the egg surface bind to molecules on the sperm surface

What do hydrolytic enzymes do when touching the egg's surface?

they make a hole in the jelly coat

What forms the acrosomal process?

growing actin filaments & proteins on the surface of the acrosomal process bind to receptors in the egg plasma membrane

REVIEW THE EGG AND SPERM STEPS ON THE SLIDES

please

Is fertilization in mammals and other terrestrial animals internal or external?

internal

What alters sperm mobility and structure?

secretions in the mammalian female reproductive tract

When must capacitation occur?

before sperm are able to fertilize an egg

Sperm travel through an outer layer of cells to reach what?

the zona pellucida, the extracellular matrix of the egg

When the sperm binds a receptor in the zona pellucida, what does it trigger?

a slow block to polyspermy

In mammals, when does the first cell division occur?

12-36 hours after sperm binding - the diploid nucleus forms after this first division of the zygote

Fusion of egg and sperm also initiates the what?

the cortical reaction, where vesicles just beneath the egg plasma membrane release their contents and form a fertilization envelope

What does the fertilization envelope act as?

the slow block to polyspermy

What does the cortical reaction require?

a high concentration of Ca2+ ions in the egg

What is another important source of developmental information?

the environment around the cell, especially signals from nearby embryonic cells

What happens in induction?

signal molecules from embryonic cells cause transcriptional changes in nearby cells, meaning interactions between cells induce differentiation of specialized cells types

What does determination do?

it commits a cell to its final fate and precedes differntiation

What is cell differentiation marked by?

the production of tissue-specific proteins

What do myblastas produce?

muscle-specific proteins and form skeletal muscle cells